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When I was younger, yogurt repulsed me. This was no small thing because my parents come from southern India, where yogurt seems to serve as a sort of digestif without which meals don’t feel complete. There was always a pot of homemade yogurt in the fridge or on the kitchen table.

Family members would marvel (and sometimes take offense) that I wasn’t finishing up my meal with yogurt, mixing it up with rice or using it to temper the spicy foods or pickles. Imagine a grandma’s Ayurvedic admonitions in place of a Robert Mitchum voiceover and a symphony of joyful slurping instead of Copland’s “Hoe-down” and you’ll have an idea of what the Yogurt, It’s What You Eat After Dinner experience was like. Some of the reasons why I was supposed to eat it:

In the comments on this weblog over the years I’ve learned a lot of interesting things about South Asian ethnography. One component which has been notable is the sense of ethnic pride of Punjabis, and in particular Jatts. Some of this is rather standard racism against other South Asians, especially South Indians and Bengalis in relation to whom they feel aesthetically superior. But other assertions of distinction are not so charged.

One of the aspects of Jatt identity seems to be the conception that they are descended from “Scythians,” what in a South Asian context would be termed Saka. When some Jatt commenters with whom I had amicable relationships with would bring this up I would gently mock them. My personal stance is that South Asians have an unhealthy obsession with presumed foreign origin, as if being South Asian is somehow shameful. This is very evident amongst Muslims for obvious reasons, insofar as Islam came to the subcontinent from West Asia. But I’ve encountered the same stance amongst Hindus. For example, Kashmiri Pandits explaining their peoples’ Persian origins.

But whatever the demerits of the excessive overall fixation on exogenous origin, I now believe that I wrongly dismissed out of hand the idea that Jatts in particular have some Scythian origin. The reason are a series of results coming out of the Harappa Ancestry Project. To be concise, it does seem that Jatts have a small but consistent proportion of northern Eurasian ancestry which sets them apart from other Punjabis. The most parsimonious explanation to my mind is that the Sakas did indeed have a genetic impact. This does not mean that I have a high confidence in this historical model. But I was clearly in the wrong in dismissing the Scythian origin myth out of hand. For that, I apologize. Also, please note that I am not claiming here that the preponderance of Jatt ancestry is Scythian. It is not. Rather, there may have been a Scythian overlay upon a typical Punjabi substrate.

We’re fast approaching the point where the “first genome” of class X is going to lose its novelty. There are more than 100 people who have had their full genome sequenced, and you can’t really track down a comprehensive list anymore that I can see. Remember, a full genome sequence is a mapping of all 3 billion DNA base pairs. In contrast, what genotyping services offer are a subset, often 1 million base pairs. The 1 million are not random, rather, they are variants which are known to…vary. But there are some important issues which can be addressed only in a full genome sequence. For example, you can see which distinct mutations are unique to you, and separate you from your parents.

Earlier this year I expressed excitement that the 1000 Genomes, “A Deep Catalog of Human Genetic Variation,” finally was going to add some more Indian populations. There was a sample of Gujaratis from Houston, but that’s a rather narrow slice of ~1 billion Indians, and nearly ~1.4 billion South Asians. The populations which were going to be added were Kayasthas from West Bengal, Marathas from Maharashtra, and Ahom from Assam.

Unfortunately, as I commented a few days ago that looks like it’s not happening. The Indian population collections have been removed from the website, and replaced by Sri Lankan Sinhalese and Tamils from the United Kingdom, and Bangladeshis. The Pakistani collection is already in process, as they’re getting the samples from Lahore. Continue reading →

I just recently heard that The Girl with the Dragon Tattoo was being made into a film. This perplexed me because I thought there was a film adaptation of that novel! Yes, there was, but that was a Swedish production, and the new film is “made in America.” Fair enough.

What does this have to do with this weblog? The actress who plays the protagonist in the Swedish film, Noomi Rapace, had a father who was a Gitano, a Spanish Romani (the term “Roma” is really an ethnonym for the eastern Romani). In case you don’t know, the Romani language is clearly Indo-Aryan. Its closeness to Indo-Aryan dialects of the Indian subcontinent is such that the story goes that Indian sailors who were stationed in Britain overheard, and understood, much of the conversation of local British Gypsies.

The origin of this population in the Indian subcontinent is evident through multiple lines of inquiry. Both in terms of culture, and genetics. Most of the genetic results focus on paternal and maternal lineages, but some “genome bloggers” have obtained samples from people with Roma background, and they clearly have distinctive South Asian ancestry. Because of intermarriage obviously this is not always visibly salient. How many people are aware that Charlie Chaplin was 1/4 Romanichal? Continue reading →

Since I began blogging here in February we’ve come a long way in getting a better sense of South Asian genetic relationships. By “we,” I’m referring mostly to Zack Ajmal of the Harappa Ancestry Project, and to a lesser extent the Dodecad Ancestry Project and the Eurogenes Genetic Ancestry Project. These explicitly amateur enterprises have taken off the shelf population genetic analytic tools, such as ADMIXTURE, and combined them with a “crowd-sourced” sampling strategy. Zack now as over 100 individuals, the vast majority of them South Asian, some from ethnicities and communities which have never been analyzed in the academic literature.

The Times of India has now taken an interest in the Harrapa Ancestry Project. I’m rather tickled by this. When I first began corresponding with Zack about the technical details of preforming this survey of South Asian genomics neither of us knew where we were going to go. The main issue we both felt needed to be addressed was of scope of sampling. In other words, there were simply too many under-sampled populations in South Asia when it came to academic analyses of the human genetics of the region.

A quick survey of a map of some participants in HAP shows that much of north-central India remains woefully under-sampled even after six months: Continue reading →

Arvind Gupta has won national awards for his many contributions to science education in India. But when he introduces himself, he calls himself a toymaker. He’s not developing the type of toys that you would buy in a store or order online. His toys are the kind people can make using trash and other everyday materials.

About two and a half months ago I brought your attention to the fact that there is population substructure in the Gujaratis of Houston. That might sound strange, but here’s the back story. Over the past ~10 years or so there has been a project attempting to catalog common human genetic variation, known as the HapMap. The HapMap began with East Asian, West African, and European groups. But over the years it has been expanding. The first South Asian population added to the database were people of Gujarati origin in Houston, Texas. Therefore, you had a situation where in the medical genetic literature there was a lot of talk about “Gujaratis from Houston,” as if that was a group of particular importance.

The ultimate pragmatic rationale for the catalog was to allow researchers to control for ancestry when attempting to fix upon genes implicated in disease. By illustration, if Chinese have disease X at a greater frequency than Europeans, if you had a common pool of Chinese + Europeans then all the genetic variants associated with the Chinese might come up as causal, when actually it’s just a correlation with ancestry. Continue reading →

The question of national and individual origins has a corporeal and concrete dimension, and a mythic and symbolic one. This is evident in the religious traditions which most of the world’s populations adhere to. Israel is both literally and figuratively a descent group. They issue from the tribes descended from the sons of Jacob. Those who convert into the Jewish religion customarily also convert into the Jewish nation, and so figuratively share the same descent. Similarly, among Muslims there is a particular prestige given over to the descendants of Muhammad, the Sayyids. Within Hinduism the importance of descent groups manifests generally in terms of the endogamy prevalent among South Asians, and also in specific cases, such as with gotras. The fundamental atomic basis of Confucian religious morality is arguably filial piety. Confucius’ descendants still play a prominent role in modern China promoting his ideas.

But descent also has a scientific and concrete aspect. Sometimes the mythic and scientific align. It does seem that the notional male line descendants of Genghis Khan are actually descended from one individual who flourished ~1,000 years ago. In other instances the connection is complex. Jews do seem to share common descent, but it is also evident that they have mixed greatly amongst the nations. And sometimes the inferences generated by science may warrant a reconsideration of treasured myths. Most reasonable people will probably accede to the clear overwhelming descent of South Asian Muslims from the native people of the Indian subcontinent, but the genetics clinches that. True, there is quite often a clear trace of Middle Eastern and African ancestry among the Muslims of South Asia above and beyond what may be found amongst non-Muslims, but often this component is dwarfed by a minor East Asian element which seems to warrant no cultural memory!
Continue reading →

I know that many people took advantage of the 23andMe sale I highlighted on Sunday. I also know that a fair number of these were brown, as I also have a list of people who I emailed, and several South Asians confirmed that they’d purchased the 23andMe kit. What do you get if you purchase this kit? Basically 1 million markers, SNPs, which are simply population-wide variant positions within your genome. These markers were chosen because variation is often informative, in terms of traits, as well as ancestry.

But obviously you are not going to just be looking at a string of letters. The data has to be analyzed for you. 23andMe provides a range of tools in this domain. But, one needs to use them cautiously, and also understand their limitations. In particular, these tools were often tuned for a specific set of populations which does not include South Asians. So some of the results are going to strike you as strange.